RNA-Seq Data Analysis: Bioinformatics Seminar

The Center for Genetic Medicine hosts a biannual bioinformatics seminar. The course is led by Matthew Schipma, PhD, Associate Director of the NUSeq Core Facility and Research Assistant Professor of Biochemistry and Molecular Genetics.

Schipma initially developed the course with former Feinberg faculty member Ann Harris, PhD at the Stanley Manne Children’s Research Institute. We aim to expand the program on the Chicago campus in order to develop this increasingly-critical skill set among students, staff, and faculty.

Course Objectives

In this course, students will learn the basic concepts of RNA-seq including principles and experimental design. Students will also develop hands-on experience in:

Registration

Registration for the spring 2018 session is now closed. Thank you for your interest in the course! We will be running the seminar again in the fall 2018.

Instructor

Matthew Schipma has over 10 years of bioinformatics experience. He holds a PhD in Biochemistry and an MS in Computer Science. He worked as a post-doctoral appointee at Argonne National Laboratory writing statistical programs to automate the analysis of biochips. Schipma then worked for Integrated Genomics Inc, where he worked in microbial genomics, DNA sequencing and assembly. Since 2010, he has been at Northwestern University in the Center for Genetic Medicine providing bioinformatics analysis for next-generation sequencing projects.

Requirements

No prior experience with RNA-Seq Data Analysis is required; the course is designed as an introduction. Attendees will need to bring a laptop to each seminar. Instructions for installing and using the required software – Xming and PuTTY – will be covered during the first seminar session. The time commitment for the seminar will be 1-3 hours per week, including class time and assigned exercises.

Curriculum

The topics covered in each session are outlined below.

Session 1: Overview and Connecting to Server

Overview of course

Introduction to analysis hardware and software

How to connect with Macbook

How to connect with PC

Session 2: Introduction to the Command Line Interface

File management

Navigating file structure

Creating directories

Deleting files/directories

Text editors

PATH and bash_profile

Symbolic links

Session 3: Considerations of Experimental Design

Library prep

mRNA vs. total RNA

strand-specificity

Depth of coverage

Number of replicates

Collection of RNA

ERCC

Session 4: Alignment Strategies

Cleaning the reads

Quality control

Genome vs. transcriptome alignment

TopHat

STAR

Session 5: Quantification

Gene expression or transcript/isoform expression

RPKM vs. read counts

Cufflinks vs. DESeq(2)

RSEM

Session 6: Advanced Analysis

Pathway analysis

Free or commercial

Promoter analysis

Gene networks

Visualization

Heat maps

Scatterplots

Connect

Please contact Matt Schipma if you have any questions regarding the seminar.

Registration

Registration for the spring 2018 session is now closed. Thank you for your interest in the course! We will be running the seminar again in the fall 2018.